mash matrix #66
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mash matrix #66
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Add new 'matrix' command which compares all input sequences and outputs a distance matrix. The current implementation is rough and ready but potentially faster than iterative 'mash dist'. fixes issue marbl#9.
… one crazy block at a time.
- pairCount is always one - parameters are unused - don't pass the maxPValue all the way down. Do that later, if interested.
Previously, for every position all 21 or so characters forming the kmer would be checked for validity. This lead to repeated checking of valid characters. I turned this into a strictly linear algorithm.
using a global PARAMETERS object now.
Thanks to @sebhtml for correcting me here. We now only hash the kmer with lower lexicographic ordering. This also reduces the total amount of kmers hashed.
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I am closing this PR now. It is just too much of a mess with little gain as there is a |
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I was frustrated with all existing solutions to produce a tree from mash distances, so I created an extra command:
mash matrix. As the name suggests, given a set of sequences it produces a distance matrix (see issue #9).Note that I tailored it specifically to my needs. This includes output sequence names (compare issue #13) and the removal of a bunch of "features" I don't care about: p-values, reading sketches might be broken, static libcapnp. You might have to cherry-pick or do some adaptation. Also, you will have to enhance the documentation.
This new tool is bloody fast: just 47 seconds to compute a distance matrix for all ~2600 E. coli from Ensembl.